Stover, which consists of the non-grain aboveground plant parts of corn (maize), sorghum, or soybean, that are left in a field after harvest, offers an abundant and inexpensive source of fermentable sugars that can be used as substrates for ethanol production. In fact, approximately upward of 275 million metric tons of stover are produced just from maize in the United States every year, two-thirds of which could be utilized for the production of ethanol, butanol, and other fuels or bioproducts (Graham, et al., (2007) “Current and potential U.S. corn stover supplies”; Agronomy Journal 99:1-11). However, the ability of cellulolytic enzymes to digest plant biomass to fermentable sugars is dependent on the properties of the plant cell wall, a highly heterogeneous and complex structure consisting of cellulose microfibrils embedded in a matrix of hemicellulose, pectin (only trace amounts in grasses), cell wall proteins, and phenolic compounds such as lignin. Lignin, in particular, being hydrophobic, significantly hinders the enzymatic hydrolysis of cellulose by preventing the swelling of cellulose fibers, thereby reducing the surface area the enzyme can access. Furthermore, it can sequester cellulases, thus preventing their action on cellulose molecules.
A similar problem arises when corn stover is used as silage. Silage is forage biomass that is harvested and fermented for use as winter fodder for cattle and sheep. As corn plants grow, the yield of energy per unit of land area increases, but the availability of energy, in the form of cellulose and hemicellulose, decreases due to lignification. This reduces the digestibility of the dry matter components in the rumen. From an economic viewpoint, the crop should be harvested at maturity, at peak dry matter yield; however, the limitation on digestibility forces harvest to take place at a more immature stage.
A promising target for the improvement of digestibility in silage maize and for the enhanced bioprocessing of corn stover for ethanol production is the lignin biosynthetic pathway. Lignin is formed by polymerization of different monolignols that are synthesized in a multistep pathway. For a more detailed review of the lignin biosynthetic pathway, see Whetton R and Sederoff R (1995) The Plant Cell, 7:1001-1013, and Whetten R et al. (1998) Annu. Rev. Plant Physiol. Plant Mol. Biol. 49:585-609. A number of studies have shown that manipulation of the number of copies of genes encoding certain enzymes in the lignin biosynthetic pathway modifies lignin quantity and quality. However, laccases, enzymes proposed to participate in the last step of lignin biosynthesis, the polymerization of monolignols (Bao et al. (1993) Science 260:672-674), have not been targeted. This is because little is known about the role of laccases in the polymerization of lignin, particularly for monocot species such as Zea mays. 
Seventeen laccase genes have been identified in the Arabidopsis genome, five of which are located in the vicinity of QTLs for the digestibility traits, Klason Lignin/Neutral Detergent Fiber (KL/NDF), KL and NDF, and DINAGZ, or the in vitro digestibility of the non starch and non soluble carbohydrates (Argillier et al. (1995) Euphytica 82:175-184; Barriere et al. (2000) Fourrages 163:221-238; Barriere et al. (2005) Plant Science 168:1235-1245). Five laccases have been identified in maize, ZmLac1, ZmLac2, ZmLac3, ZmLac4, and ZmLac5. However, while the expression patterns of at least four of these genes (ZmLac2, ZmLac3, ZmLac4, and ZmLac5) correlate with maize regions undergoing lignification, no direct link between laccases and lignin polymerization has been established (Caparros-Ruiz et al. (2006) Plant Science 171:217-225).
Genes that increase cell wall digestibility can be employed in breeding programs by the introgression of the most valuable alleles at these loci. Hence, it is desirable to provide allelic compositions and methods for identifying maize plants that display increased cell wall digestibility. Plants with increased cell wall digestibility will have enhanced biomass conversion efficiency for ethanol production, and will also have improved silage quality.